Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 27, Issue 14, Pages 1693-1702Publisher
WILEY
DOI: 10.1002/jcc.20473
Keywords
molecular dynamics; chemical flooding; conformational flooding; enhanced sampling; transition path prediction; QM/MM; umbrella sampling
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The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to microseconds time scales or faster can be studied directly. Unfortunately, apart from a few exceptions, relevant processes, such as chemical reactions or many large scale conformational transitions in proteins, occur at slower time scales and therefore are currently far out of reach for conventional MD. The flooding technique addresses this problem by inclusion of a flooding potential into the force field. This flooding potential locally destabilizes the educt state and thereby significantly accelerates the escape from the initial energy well without affecting the reaction pathway. Here, we summarize the theory and method for the computational chemistry community and detail the implementation within the official version 3.3 of the freely available MD program package GROMACS. Two examples shall demonstrate the application of flooding to accelerate conformational transitions and chemical reactions. The second example was carried out within a QM/MM framework. (C) 2006 Wiley Periodicals, Inc.
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